16-84833396-T-C

Variant names:

• chr16-84833396-T-C
• rs8051428
• NM_031476.4:c.-74-5026T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_031476.4(CRISPLD2):​c.-74-5026T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.368 in 152,096 control chromosomes in the GnomAD database, including 10,642 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.37 (10642 hom., cov: 32)
• Consequence: CRISPLD2 NM_031476.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 3 publications found

Genes affected

CRISPLD2 (HGNC:25248): (cysteine rich secretory protein LCCL domain containing 2) Predicted to enable glycosaminoglycan binding activity. Involved in face morphogenesis. Located in transport vesicle. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000285848 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031476.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRISPLD2	NM_031476.4	MANE Select	c.-74-5026T>C		intron	N/A	NP_113664.1	Q9H0B8-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRISPLD2	ENST00000262424.10	TSL:1 MANE Select	c.-74-5026T>C		intron	N/A	ENSP00000262424.5	Q9H0B8-1
	CRISPLD2	ENST00000564567.5	TSL:1	c.-74-5026T>C		intron	N/A	ENSP00000457655.1	Q9H0B8-2
	CRISPLD2	ENST00000569090.1	TSL:1	c.-74-5026T>C		intron	N/A	ENSP00000454858.1	Q9H0B8-5

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55810 AN: 151978 Hom.: 10615 Cov.: 32

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.366

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.368 AC: 55905 AN: 152096 Hom.: 10642 Cov.: 32 AF XY: 0.364 AC XY: 27059 AN XY: 74392

African (AFR) AF: 0.458 AC: 18972 AN: 41458

American (AMR) AF: 0.408 AC: 6233 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1347 AN: 3462

East Asian (EAS) AF: 0.114 AC: 591 AN: 5172

South Asian (SAS) AF: 0.320 AC: 1544 AN: 4826

European-Finnish (FIN) AF: 0.290 AC: 3075 AN: 10600

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22851 AN: 67988

Other (OTH) AF: 0.370 AC: 781 AN: 2110

Alfa AF: 0.356 Hom.: 17796

Bravo AF: 0.380

Asia WGS AF: 0.276 AC: 964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	3.1
DANN	Benign	0.82
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs8051428; hg19: chr16-84867002;